Symmetry App© – Getting Started

Double click on the jar file to begin execution. The following 3 easy steps are all that is involved in using the program. Links to screen captures (SC#) of numerous procedures are listed.

1. From the File pulldown menu, choose Open (SC1) and browse your file structure until you find the library (SC2) that was downloaded. Alternatively, you can select a file that contains the Cartesian coordinates of any molecule of interest. The file must have the total number of atoms listed on the first line, a title on the second line (or the line may be blank), and all remaining lines contain the atomic number or atomic symbol (case insensitive) followed by the x y and z coordinates (in Angstrom units, space delimited). Click here (SC3) for a screen capture showing the input of the diborane example molecule.
2. Inspect the molecule you’ve opened to decide what type of symmetry element you will define – the identity, an inversion center, a proper rotation axis, an improper rotation axis, or a mirror plane. Recall that an inversion center is defined by specifying a single point in space, a rotation axis is defined by specifying two points, and a mirror plane is defined by three. Nothing needs to be defined for the identity.When defining your symmetry element, there are two possible scenarios. Either (a) the atoms of your molecule are in positions that will allow you to define your symmetry element relative to these atoms, or (b) they are not, and “dummy” atoms will need to be specified to define the symmetry element.Case (a): If the atoms of your molecule are in positions that allow you to define the symmetry element relative to these atoms, go to the Symmetry pulldown menu and select which of the 5 symmetry elements you wish to define (SC4). For all but the Identity, a popup window appears with dynamic instructions requesting additional information. Such information includes the selection of atoms (by clicking on them) in the molecule to define the symmetry element (a point, line or plane) (SC5, SC6, SC7).

   Case (b): If additional points (“dummy atoms”) are needed to define the symmetry element, go to the Define pulldown menu and select from the list. From this list, you can define a dummy atom at the midpoint between two existing points (SC8), the centroid of any polygon (i.e. ‘ring’ of atoms), or a perpendicular to a line or a polygon (ring) (SC9). Note that dummy atoms that have already been defined can themselves be used as reference points when defining subsequent midpoints, centroids or perpendiculars.

3. Execute the desired symmetry operation by clicking the Rotate, Reflect, Invert, or Rotate/Reflect for the proper rotation axis, mirror plane, inversion center, or improper rotation axis, respectively (SC10). The identity operation is carried out without further options.Once the symmetry operation has been executed, a second window appears in which both images – the original image and that after the symmetry operation has been applied – are superimposed on each other (SC11). If the symmetry element was valid for the molecule, the images will be perfectly superimposed, and the program will list red text at the bottom of the window “The selected symmetry element IS present.” If the symmetry element was not valid, the images will not be a perfect superposition, and the program will list red text at the bottom of the window “The selected symmetry element IS NOT present.” An example of this is given in the following set of screen captures where a C3 rotation axis has been defined at the two bridging hydrogens of diborane (SC12) and executed (SC13).To define a C2 rotation axis that is perpendicular to the plane of borons and bridging hydrogens, two dummy atoms are needed. The first of these should reside midway between the two boron atoms. The dummy atom is created by selecting Midpoint from the Define pulldown menu (SC8) and, following the dynamic instructions (in red) at the bottom of the screen (SC14), selecting the two boron atoms (SC15). Click the Go! button found in the bottom right corner of the window to place the dummy atom in the molecule (SC16). The second dummy atom can be defined as a point perpendicular to the ring of bridging hydrogens and borons. Select Perpendicular To A Ring from the Define pulldown menu (SC9) and, again, follow the dynamic instructions (in red) at the bottom of the screen (SC17). Once the atoms in the ring are selected (terminating the selection by clicking on the first atom in the ring for a second time), click the Go! button to place the dummy atom (SC18).

   When you want to select another molecule from the library or from another source, Close the current molecule selection (File pulldown, SC19) so that Open will be active in the File pulldown menu.

   Defining/executing other symmetry elements/operations proceeds in a similar manner, where the dynamic instructions guide the user through the process.